A name to attach to the origins of the manuscript

[Jorge_Stolfi]

90% of people then were illiterate.

10% is still vastly more than the people from that time that we know something about...

The author(s) of the Voynich seem to be someone who was very educated

He was educated, probably.  But "very"?  I don't see why...

The fact that the Author invented a very distinctive script and wanted to have a book written with it tell us that he was a "scholar", but only in the  very broad sense by which Marco Polo and the Rohonc author were "scholars".  The breadth of topics, and the very distinctive formats of each section suggests that he was not writing his own knowledge or experience, but was copying/translating/summarizing other books.  

We now know that the Scribe was copying figures from other European books, and we have even identified some of those books.  But apparently he did not understand what he was copying.  So probably those books were provided by the Author.  In all, I think we can say only that the Author was at home among books. 

On the other hand, if we ignore the decoration and figure details that were probably cribbed by the Scribe from other books, the actual contents of the VMS seems quite "alien".  For instance, some of the illustrations of Bio may have been cribbed from the Balneis Puteolarum, but then others can only be about human anatomy. 

Thus it does not seem that he was part of the community of scholars of the time, in the Church or outside it.  He may have been a "genius of the first class" in the sense of Lem's story...

he must have been quite wealthy to have afforded the vellum and inks needed for the manuscript

On the contrary. As Lisa already noted, the vellum is of poor quality and he used every inch of it, down to its irregular edges.  The Scribe(s) that he recruited were not professional and apparently had no experience writing illustrated books.  Or maybe books of any kind.  And I have reasons to believe that the Scribe(s) had never written on vellum before.

If the manuscript is written in cipher as most Voynich researchers have said they believe in a survey then the author could well have been particularly well educated and able to produce such a difficult cipher to crack.

No "cipher" is as hard to "crack" than a language that is not related to any that you know.  Especially if it is written in an letters that you don't even know the sounds of.  I could stare at a book in Georgian, Malayalam, or Berber for my whole life and not make any sense of it.  

So, for me, the fact that the "cipher" has resisted 80 years of computer-assisted analysis is strong evidence that the underlying language is not "European".  In which case it would not need to be encrypted at all...

All the best, --stolfi